Delaney Sullivan
Delaney Sullivan
OK, yes, rna velocity is just slow with kallisto. This will change in our forthcoming release of kb-python (version 0.28; currently on devel branch), which will be released in the...
Currently, kb count only does transcript quantification for bulk/smart-seq data (where each sample or cell is in a separate FASTA file). For 10X type data, kb count stops at the...
Oh, with such a large matrix, it's computationally intractable. You will definitely need to filter cells. The EM algorithm (which gives you transcript counts) in quant-tcc only takes a few...
No, kallisto is fine for that purpose (and was actually initially designed for full gene lengths)
1. What version are you running? 2. What are you generating a loom file for? 3. As mentioned in multiple other GitHub issues, Signals.SIGILL: 4 typically means you have to...
Sounds good -- install kallisto from source, and also, upgrade kb-python to the latest version (0.28.2).
You can use the prebuilt indices (they contain lncRNA targets and kb ref uses “kallisto index” under the hood anyway). However, if you use those, make sure you’re using the...
Thanks! I think there's two things that always results in some compilations issues: 1) The AVX-2 instructions, and 2) machine architecture (march) option. These optimizations are enabled by default (in...
Unfortunately not yet; haven't really prioritize it since kallisto works on most (albeit not all) systems. As such, a new release will include more than just these upgrades to the...